CN109311920A

CN109311920A - The method for preparing phosphoric acid diamides morpholino oligomers

Info

Publication number: CN109311920A
Application number: CN201780030642.8A
Authority: CN
Inventors: B.蔡; M.马蒂尼; R.施马布库; K.托马斯
Original assignee: SA Leputa Medical Co
Current assignee: SA Leputa Medical Co
Priority date: 2016-05-24
Filing date: 2017-05-24
Publication date: 2019-02-05
Anticipated expiration: 2037-05-24
Also published as: US10961262B2; PL3464306T3; JP2019523754A; KR102504759B1; CN109311920B; AU2017271524B2; PT3464306T; RS65504B1; FI3464306T3; IL263033B2; DK3464306T3; CA3024182A1; AU2017271524A1; SG11201809499UA; TW201825506A; WO2017205513A1; EP3464306A1; SI3464306T1; BR112018074270B1; LT3464306T

Abstract

There is provided herein the methods for preparing oligomer (such as morpholino oligomers).Synthetic method as described herein can be conducive to amplify oligomer synthesis, while keep the gross production rate and purity of synthesis oligomer.

Description

Process for preparing phosphoric acid diamide morpholino oligomer

RELATED APPLICATIONS

The present application claims the benefit of U.S. provisional patent application No.62/340,953 filed on 24/2016 and U.S. provisional patent application No.62/357,134 filed on 30/6/2016, each of which is incorporated herein by reference in its entirety.

Background

Antisense technology provides a means of modulating the expression of one or more specific gene products, including alternative splicing products, and is uniquely useful in a number of therapeutic, diagnostic and research applications. The principle behind antisense technology is that antisense compounds, e.g., oligonucleotides, that hybridize to a target nucleic acid modulate gene expression activity, e.g., transcription, splicing, or translation, by any of a number of antisense mechanisms. The sequence specificity of antisense compounds makes them attractive as tools for target validation and gene functionalization, as well as therapeutic agents that selectively modulate the expression of genes involved in disease.

Duchenne Muscular Dystrophy (DMD) is caused by a defect in the expression of the protein dystrophin protein. The gene encoding this protein contains 79 exons, distributed over more than 200 ten thousand DNA nucleotides. Any exon mutation, which alters the reading frame of an exon, or introduces a stop codon, or is characterized by deletion of one or several exons outside the entire frame, or one or more repeats of an exon, may disrupt the production of functional dystrophin, resulting in DMD.

Recent clinical trials testing the safety and efficacy of Splice Switching Oligonucleotides (SSOs) for the treatment of DMD are based on the SSO technique, inducing alternative splicing of pre-mRNA by spatial blocking of spliceosomes (Cirak et al, 2011; Goemans et al, 2011; Kinali et al, 2009; van Deutekom et al, 2007). However, despite these successes, the pharmacological options available for treating DMD are limited.

Eteplirsen is a Phosphodiamide Morpholino Oligomer (PMO) designed to skip exon 51 of the human dystrophin gene in DMD patients, who can correct to exon 51 skipping to restore reading frame and produce a functionally shorter form of dystrophin. Sarepta Therapeutics, inc, filed a New Drug Application (NDA) to the united states Food and Drug Administration (FDA) seeking approval for the treatment of DMD in patients who can correct exon 51 skipping. NDA of Sarepta is currently being reviewed by the FDA.

Despite the significant advances made in the field of antisense technology, there remains a need in the art for methods of making phosphodiamide morpholino oligomers with improved antisense or antigenic properties.

Disclosure of Invention

Provided herein are methods for preparing Phosphorodiamidite Morpholino Oligomers (PMOs). The synthetic methods described herein can scale up PMO synthesis while maintaining the overall yield and purity of the synthesized PMO.

Accordingly, in one aspect, provided herein is a method of making an oligomeric compound of formula (a):

in certain embodiments, provided herein are methods of making oligomeric compounds of formula (E):

in other embodiments, the oligomeric compounds of the present disclosure include, for example, some embodiments of the oligomeric compound of formula (E), which is an oligomeric compound of formula (XII):

for clarity, the formulae including, for example, oligomeric compounds of formula (E) and Eteplirsen of formula (XII) are sequential formulae from 5 'to 3', and for convenience in describing the entire formula in a compact form in the above formulae, applicants have labeled various schematic cleavas as "breka", "brekb", "BREAK C", and "brekd". As understood by those skilled in the art, for example, each schematic "BREAK A" represents a schematic in which the structural formula continues at these points. The same is understood by those skilled in the art to be true for each instance of "BREAK B", "BREAK C", and "BREAK D" in the above formulae including Eteplirsen. In any event, none of the schematic cleavages is intended to indicate that the skilled artisan would not believe it would mean a realistic cleavage of the above-described structural formulae including Eteplirsen.

Drawings

FIG. 1 shows representative analytical High Performance Liquid Chromatography (HPLC) chromatograms of synthetic and deprotected Eteplissen (AVI-4658) starting drug substrate (see example 4).

Figure 2 shows a representative analytical HPLC chromatogram of a purified Eteplirsen drug solution (see example 5).

Figure 3 shows a representative analytical HPLC chromatogram of desalted and lyophilized Eteplirsen drug (see example 5).

Detailed Description

Provided herein are methods of making morpholino oligomers. The morpholino oligomers described herein exhibit greater affinity for DNA and RNA relative to native or unmodified oligonucleotides without compromising sequence selectivity. In some embodiments, the morpholino oligomers of the present disclosure minimize or prevent cleavage by rnase H. In some embodiments, the morpholino oligomer of the present disclosure does not activate rnase H.

The methods described herein are advantageous in industrial-scale processes and can be applied to the preparation of an amount of morpholino oligomer (e.g., about 1kg, about 1-10kg, about 2-10kg, about 5-20 kg, about 10-20 kg, or about 10-50 kg) in high yield and scale.

Definition of

Listed below are definitions of various terms used to describe the present disclosure. These definitions apply to the terms used throughout the specification and claims, unless otherwise defined individually or as part of a larger group in specific instances.

"base-protected" or "base protection" refers to the protection of a base-pairing group, such as a purine or pyrimidine base, on a morpholino subunit, wherein the protecting group is adapted to prevent reaction or interference of the base-pairing group during stepwise synthesis of the oligomer. (an example of a base-protected morpholino subunit is an activated C subunit compound (C) having a CBZ protecting group on the cytosine amino group described below).

The "activated phosphoramidate group" is typically a chlorophosphamide ester group with a substitution on the nitrogen, which is required for the final phosphoramidate linkage in the oligomer. An example is (dimethylamino) chlorophosphoramide ester, i.e., -O-P (═ O) (NMe2) Cl.

The term "carrier-bound" refers to a chemical entity covalently attached to a carrier medium.

The term "support medium" refers to any material to which an oligomer can be attached or synthesized, or which can be modified for use in connection with or synthesizing an oligomer, including, for example, any particle, bead, or surface. Representative substrates include, but are not limited to, inorganic and organic supports such as glass and modified or functionalized glass, plastics (including acrylics, polystyrenes and copolymers of styrene and other materials, polypropylene, polyethylene, polybutylene, polyurethane, teflon, and the like), polysaccharides, nylon or nitrocellulose, ceramics, resins, silica or silica-based materials (including silicon and modified silicon), carbon, metals, inorganic glass, plastics, fiber optic strands, and various other polymers. For some embodiments, particularly useful carrier media and solid surfaces are located within a flow cell device. In some embodiments of the methods described herein, the support medium comprises polystyrene with 1% cross-linked divinylbenzene.

In some embodiments, a representative carrier medium comprises at least one reactive site for linking or synthesizing an oligomer. For example, in some embodiments, the carrier medium of the present disclosure comprises one or more terminal amino or hydroxyl groups capable of forming a chemical bond with an incoming subunit or other activating group for linking or synthesizing an oligomer.

Some representative carrier media suitable for the methods described herein include, but are not limited to, Controlled Pore Glass (CPG), oxalyl controlled pore glass (see, e.g., Allol et al, Nucleic Acids Research1991,19,1527), silica-containing particles (e.g., porous glass beads) and silica gel, such as particles formed by the reaction of trichloro- [3- (4-chloromethyl) phenyl ] propyl silane and porous glass beads (see Parr and Grohmann, Angew. chem. internal. Ed.1972,11,314, sold by Waters Associates under the trademark "PORASIL E", Framingham, Mass., USA), monoesters of 1, 4-dihydroxymethylbenzenes and silica (see Bayer and Jung, Tetrahedron Lett.,1970,4503, sold by Waters Associates under the trademark "OPNTAK", TENTAGAGAGE (see, e.g, TETRA et al, TETRAHEDRODON Lett., USA, 198577, 19857), and polyethylene glycol grafted with a polyethylene glycol grafted polyethylene glycol, ethylene graft copolymer (see, ethylene graft copolymers of ethylene glycol, ethylene graft copolymers, ethylene glycol, ethylene graft membranes, ethylene graft polymers, ethylene glycol, ethylene graft polymers, ethylene graft copolymers, ethylene, propylene graft copolymers, ethylene, propylene, ethylene, polyethylene, propylene, polyethylene.

The term "flow cell device" refers to a chamber comprising a surface (e.g., a solid surface) through which one or more fluid reagents (e.g., liquids or gases) can flow.

The term "deblocking agent" refers to a composition (e.g., a solution) comprising a chemical acid or combination of chemical acids for removal of a protecting group. Exemplary chemical acids for the deblocking agent include halogenated acids such as chloroacetic acid, dichloroacetic acid, trichloroacetic acid, fluoroacetic acid, difluoroacetic acid, and trifluoroacetic acid. In some embodiments, the deblocking agent removes one or more trityl groups from, for example, an oligomer, a carrier-bound subunit, or other protected nitrogen or oxygen moieties.

The terms "halogen" and "halo" refer to an atom selected from fluorine, chlorine, bromine, and iodine.

The term "capping agent" refers to a composition (e.g., solution) comprising an anhydride (e.g., benzoic anhydride, acetic anhydride, phenoxyacetic anhydride, etc.) that can be used to block, for example, reactive sites of a support medium from forming chemical bonds with incoming subunits or other activating groups.

The term "lysing agent" refers to a composition comprising a chemical base (e.g., ammonia or 1, 8-diazabicycloundec-7-ene) or a combination of chemical bases (e.g., a liquid solution or a gas mixture) that is used to lyse a carrier-bound oligomer, e.g., from a carrier medium.

The term "deprotecting agent" refers to a composition comprising a chemical base (e.g., ammonia, 1, 8-diazabicycloundecen-7-ene, or potassium carbonate) or a combination of chemical bases (e.g., a liquid solution or a gas mixture) that can be used to remove protecting groups. For example, in some embodiments, the deprotection agent can remove a base protecting group from, for example, a morpholino subunit of a morpholino oligomer, or a carrier-bound form thereof.

The term "solvent" refers to a component of a solution or mixture in which a solute is dissolved. The solvent may be inorganic or organic (e.g., acetic acid, acetone, acetonitrile, acetylacetone, 2-aminoethanol, aniline, anisole, benzene, benzonitrile, benzyl alcohol, 1-butanol, 2-butanol, isobutanol, 2-butanone, t-butanol, carbon disulfide, carbon tetrachloride, chlorobenzene, chloroform, cyclohexane, cyclohexanol, cyclohexanone, di-n-butyl phthalate, 1-dichloroethane, 1, 2-dichloroethane, diethylamine, diethylene glycol dimethyl ether, dimethoxyethane (glyme), N, N-dimethylaniline, dimethylformamide, dimethyl phthalate, dimethyl sulfoxide, dioxane, ethanol, diethyl ether, ethyl acetate, ethyl acetoacetate, ethyl benzoate, ethylene glycol, glycerol, heptane, 1-heptanol, hexane, 1-hexanol, xylene, or the like, Methanol, methyl acetate, methyl tert-butyl ether, methylene chloride, 1-octanol, pentane, 1-pentanol, 2-pentanol, 3-pentanol, 2-pentanone, 3-pentanone, 1-propanol, 2-propanol, pyridine, tetrahydrofuran, toluene, water, p-xylene).

The phrases "morpholino oligomer" and "phosphodiamide morpholino oligomer" or "PMO" refer to oligomers having morpholino subunits linked together by a phosphodiamide, linking the morpholino nitrogen of one subunit to the 5' -exocyclic carbon of an adjacent subunit. Each morpholino subunit comprises a nucleobase-pairing moiety that effectively binds to a nucleobase in a target through nucleobase-specific hydrogen bonding.

The term "EG 3 tail" refers to a triethylene glycol moiety conjugated to an oligomer, for example at the 3 'or 5' end thereof. For example, in some embodiments, the "EG 3 tail" conjugated to the 3' end of the oligomer may have the following structure:

the term "about" or "approximately" is generally understood by those skilled in the relevant subject matter art, but may in some cases mean within ± 10% or ± 5% of a given value or range.

Process for preparing morpholino oligomers

The synthesis is typically prepared on a support medium, as described herein. Typically, a first synthon (e.g., a monomer, such as a morpholino subunit) is first attached to a carrier support medium, and then an oligomer is synthesized by sequentially coupling the subunits to the carrier-bound synthon. This iterative extension ultimately yields the final oligomeric compound. Suitable carrier media may be soluble or insoluble, or may have variable solubility in different solvents, so that the growing carrier-bound polymer is in or out of solution as desired. Conventional support media are largely insoluble and are routinely placed in a reaction vessel while reagents and solvents are reacted and/or washed with the growing chain until the oligomer reaches a target length, after which it is cleaved from the support and, if necessary, further worked up to produce the final polymeric compound. Recent approaches have introduced soluble supports, including soluble polymeric supports, to allow precipitation and dissolution of the product of repeated syntheses at the desired point in the synthesis (Gravert et al, chem. Rev.,1997,97, 489-510).

Provided herein are methods of making morpholino oligomers.

Accordingly, in one aspect, provided herein is a process for preparing a compound of formula (II):

wherein R is¹Is a carrier medium;

wherein the process comprises contacting (A1) the compound with a deblocking agent:

wherein R is¹Being a carrier medium, R³Selected from the group consisting of trityl, monomethoxytrityl, dimethoxytrityl and trimethoxytrityl,

to form a compound of formula (II).

In another aspect, provided herein is a process for preparing a compound of formula (a 3):

wherein R is¹Is a carrier medium, R³Selected from trityl, monomethoxytrityl, dimethoxytritylAnd trimethoxytrityl;

wherein the process comprises reacting a compound of formula (II):

wherein R is¹Is a carrier medium for the carrier medium,

a compound of contact (a 2):

wherein R is³Selected from the group consisting of trityl, monomethoxytrityl, dimethoxytrityl and trimethoxytrityl,

to form the compound of formula (a 3).

In another aspect, provided herein is a process for preparing a compound of formula (IV):

wherein R is¹Is a carrier medium;

wherein the process comprises contacting (A3) the compound with a deblocking agent:

wherein R is¹Is a carrier medium, R³Selected from the group consisting of trityl, monomethoxytrityl, dimethoxytrityl and trimethoxytrityl;

to form the compound of formula (IV).

In another aspect, provided herein is a process for preparing a compound of formula (a 5):

wherein R is¹Is a carrier medium, R³Selected from the group consisting of trityl, monomethoxytrityl, dimethoxytrityl and trimethoxytrityl, and

R⁴selected from:

wherein the method comprises reacting a compound of formula (IV):

wherein R is¹Is a carrier medium for the carrier medium,

compound of contact (a 4):

wherein R is³Selected from the group consisting of trityl, monomethoxytrityl, dimethoxytrityl and trimethoxytrityl, R⁴Selected from:

to form the compound of formula (a 5).

In another aspect, provided herein is a process for preparing a compound of formula (a 9):

wherein n is an integer of 10 to 40, R¹Is a carrier medium, R³Selected from trityl, monomethoxytrityl, dimethoxytrityl and trimethoxypentyl, and R⁴Each occurrence is independently selected from:

and

wherein the method comprises the following sequential steps:

(a) reacting a compound of formula (IV):

wherein R is¹Is a carrier medium;

compound of contact (a 4):

to form a compound of formula (a 5):

R⁴selected from:

and

(b) n-1 iterations of the following sequential steps are performed:

(b1) contacting the product formed in the previous step with a deblocking agent; and is

(b2) Contacting the compound formed in the previous step with (A8) a compound:

wherein R is³Selected from the group consisting of trityl, monomethoxytrityl, dimethoxytrityl and trimethoxytrityl, and for each compound of formula (A8), R is⁴Independently selected from:

to form the compound of formula (a 9).

In another aspect, provided herein is a process for preparing a compound of formula (a 10):

wherein n is an integer of 10 to 40, R¹Is a carrier medium, R⁴Each occurrence is independently selected from:

wherein the process comprises contacting the deblocking agent with (A9) a compound:

to form the compound of formula (a 10).

In another aspect, provided herein is a process for preparing a compound of formula (a 11):

wherein n is an integer of 10 to 40, R⁴Each occurrence is independently selected from

Wherein the process comprises reacting a compound of formula (A10):

with a cleaving agent to form a compound of formula (A11).

In another aspect, provided herein is a method of making an oligomeric compound of formula (a):

wherein n is an integer of 10 to 40, and each R²Independently at each occurrence is selected from:

wherein the process comprises contacting a compound of formula (a 11):

wherein n is an integer of 10 to 40, R⁴Each occurrence is independently selected from:

to form the oligomeric compound of formula (A).

wherein the method comprises the following sequential steps:

(a) contacting (a1) compound with deblocking agent:

to form a compound of formula (II):

wherein R is¹Is a carrier medium;

(b) contacting a compound of formula (II) with a compound of formula (a 2):

to form a compound of formula (a 3):

(c) contacting (a3) a compound with a deblocking agent to form a compound of formula (IV):

wherein R is¹Is a carrier medium;

(d) contacting a compound of formula (IV) with a compound of formula (a 4):

to form a compound of formula (a 5):

R⁴selected from:

(e) n-1 iterations of the following sequential steps are performed:

(e1) contacting the product formed in the previous step with a deblocking agent; and is

(e2) Contacting the compound formed in the previous step with (A8) a compound:

to form a compound of formula (a 9):

and

(f) contacting a compound of formula (a9) with a deblocking agent to form a compound of formula (a 10):

(g) contacting a compound of formula (a10) with a cleaving agent to form a compound of formula (a 11):

and

(h) contacting the compound of formula (a11) with a deprotection agent to form an oligomeric compound of formula (a).

In one embodiment, step (d) or step (e2) further comprises contacting the compound of formula (IV) or the compound formed in the previous step, respectively, with an endcapping agent.

In another embodiment, each step is carried out in the presence of at least one solvent.

In another embodiment, the deblocking agent used in each step is a solution comprising a halogenated acid.

In another embodiment, the deblocking agent used in each step is cyanoacetic acid.

In another embodiment, the halogenated acid is selected from the group consisting of chloroacetic acid, dichloroacetic acid, trichloroacetic acid, fluoroacetic acid, difluoroacetic acid, and trifluoroacetic acid.

In another embodiment, the halogenated acid is trifluoroacetic acid.

In another embodiment, at least one of steps (a), (c), (e1), and (f) further comprises the step of contacting the deblocking compound of each step with a neutralizing agent.

In yet another embodiment, each of steps (a), (c), (e1), and (f) further comprises the step of contacting the deblocking compound of each step with a neutralizing agent.

In another embodiment, the neutralizing agent is in a solution comprising dichloromethane and isopropanol.

In another embodiment, the neutralizing agent is a monoalkyl, dialkyl or trialkyl amine.

In another embodiment, the neutralizing agent is N, N-diisopropylethylamine.

In another embodiment, the deblocking agent used in each step is a solution comprising 4-cyanopyridine, dichloromethane, trifluoroacetic acid, trifluoroethanol, and water.

In another embodiment, the capping agent is in a solution comprising ethylmorpholine and methylpyrrolidone.

In another embodiment, the capping agent is an anhydride.

In another embodiment, the anhydride is benzoic anhydride.

In another embodiment, the compounds of formula (a4) and formula (A8) are each independently a solution comprising ethyl morpholine and dimethyl imidazolidinone.

In another embodiment, the cleavage agent comprises dithiothreitol and 1, 8-diazabicyclo [5.4.0] undec-7-ene.

In another embodiment, the lysing agent is in a solution comprising N-methyl-2-pyrrolidone.

In yet another embodiment, the deprotection agent comprises NH₃。

In another embodiment, the deprotecting agent is in aqueous solution.

In another embodiment, the support medium comprises polystyrene with 1% cross-linked divinylbenzene.

In another embodiment, the compound of formula (A4) has the formula (A4 a):

wherein R is³Selected from the group consisting of trityl, monomethoxytrityl, dimethoxytrityl and trimethoxytrityl, and R⁴Selected from:

in another embodiment, the compound of formula (A5) has the formula (A5 a):

wherein:

R¹is a carrier medium for the carrier medium,

R³selected from the group consisting of trityl, monomethoxytrityl, dimethoxytrityl and trimethoxytrityl, and

R⁴selected from:

in another embodiment, the compound of formula (A8) has the formula (A8 a):

wherein:

R⁴each occurrence in formula (A8a), independently selected from:

in another embodiment, the compound of formula (A9) has the formula (A9 a):

wherein:

n is an integer of 10 to 40,

R¹is a carrier medium for the carrier medium,

R⁴each occurrence is independently selected from:

in another embodiment, the compound of formula (a10) has the formula (a10 a):

wherein,

n is an integer of 10 to 40,

R¹is a carrier medium, and

R⁴each occurrence is independently selected from:

in another embodiment, the compound of formula (a11) has the formula (a11 a):

wherein:

n is an integer of 10 to 40, and

R⁴each occurrence is independently selected from:

in another embodiment, wherein for the oligomeric compound of formula (A), n is 30, and R is²Each position from 1 to 30 and 5 'to 3' is:

position 5 'to 3'	R²	Position 5 'to 3'	R²	Position 5 'to 3'	R²
						1	C	11	A	21	G
2	T	12	A	22	C
						3	C	13	G	23	A
4	C	14	G	24	T
						5	A	15	A	25	T
6	A	16	A	26	T
						7	C	17	G	27	C
8	A	18	A	28	T
						9	T	19	T	29	A
10	C	20	G	30	G

Wherein the oligomeric compound of formula (A) is a compound of formula (E):

or a pharmaceutically acceptable salt thereof

Eteplirsen (see, e.g., international patent application publication No. WO2006/000057, incorporated herein by reference in its entirety) has been the subject of clinical research to test its safety and efficacy, and is undergoing clinical development. Eteplirsen is a phosphoric acid diamide morpholino oligomer (PMO). The dystrophin therapeutic "Eteplirsen", also known as "AVI-4658", is a PMO having base sequence 5'-CTCCAACATCAAGGAAGATGGCATTTCTAG-3' (SEQ ID NO: 1). Etepliersen has CAS registry number 1173755-55-9. The chemical names include: RNA, [ P-deoxy-P- (dimethylamino) ] (2',3' -dideoxy-2 ',3' -imino-2 ',3' -seco) (2' a → 5') (C-m5U-C-C-A-A-C-A-m 5U-C-A-G-A-m 5U-G-C-A-m 5U-m5U-m5U-C-m5U-A-G) (SEQ ID NO:1), 5' - [ P- [4- [ [2- [2- (2-hydroxyethoxy) ethoxy ] carbonyl ] -1-piperazinyl ] -N, n-dimethylphosphineamide ester ] and P,2',3' -trideoxy-P- (dimethylamino) -5' -O- { P- [4- (10-hydroxy-2, 5, 8-trioxadecanoyl) piperazin-1-yl ] -N, N-dimethylphosphineamide } -2',3' -imino-2 ',3' -secocytidylyl- (2' a → 5') -P,3' -dideoxy-P- (dimethylamino) -2',3' -imino-2 ',3' -secothymidine-yl- (2' a → 5') -P,2',3' -trideoxy-P- (dimethylamino) -2',3 '-imino-2', 3 '-secocytidinoyl- (2' a → 5') -P,2',3 '-trideoxy-P- (dimethylamino) -2',3 '-imino-2', 3 '-secoadenylyl- (2' a → 5') -P,2',3 '-trideoxy-P- (dimethylamino) -2',3' -imino-2 ',3' -secocytidinoyl- (2' a → 5') -P,2',3' -trideoxy-P- (dimethylamino) -2',3' -imino-2 ',3' -secoadenylyl- (2' a → 5') -P,3' -dideoxy-P- (dimethylamino) -2',3' -imino-2 ',3' -secothymidine acyl- (2' a → 5') -P,2',3' -trideoxy-P- (dimethylamino) -2',3' -imino-2 ',3' -secocytidinoyl- (2' a → 5') -P,2',3' -trideoxy-P- (dimethylamino) -2',3 '-imino-2', 3 '-secoadenylyl- (2' a → 5') -P,2',3 '-trideoxy-P- (dimethylamino) -2',3 '-imino-2', 3 '-secoguanonyl- (2' a → 5') -P,2',3 '-trideoxy-P- (dimethylamino) -2',3' -imino-2 ',3' -secoadenylyl- (2' a → 5') -P,2',3' -trideoxy-P- (dimethylamino) -2',3' -imino-2 ',3' -secoguanoylyl- (2' a → 5') -P,2',3' -trideoxy-P- (dimethylamino) -2',3' -imino-2 ',3' -secoadenylyl- (2' a → 5') -P,3' -dideoxy-P- (dimethylamino) -2',3 '-imino-2', 3 '-secothymidine acyl- (2' a → 5') -P,2',3 '-trideoxy-P- (dimethylamino) -2',3 '-imino-2', 3 '-secoguanoyl- (2' a → 5') -P,2',3 '-trideoxy-P- (dimethylamino) -2',3 '-imino-2', 3 '-secocytidine- (2' a → 5') -P,2',3 '-trideoxy-P- (dimethylamino) -2',3' -imino-2 ',3' -secoadenylyl- (2' a → 5') -P,3' -dideoxy-P- (dimethylamino) -2',3' -imino-2 ',3' -secothymidine acyl- (2' a → 5') -P,2',3' -trideoxy-P- (dimethylamino) -2',3 '-imino-2', 3 '-secocytidylcytidyl- (2' a → 5') -P,3' -dideoxy-P- (dimethylamino) -2',3' -imino-2 ',3' -secothymidine acyl- (2'a → 5') -P,2',3' -trideoxy-P- (dimethylamino) -2',3' -imino-2 ',3' -secoadenylyl- (2'a → 5') -2',3' -dideoxy-2 ',3' -imino-2 ',3' -secoguanosine.

Eteplirsen has the following structure:

eteplirsen can also be described by the structure of formula (XII):

thus, in one embodiment of the above process, the oligomeric compound of formula (a) is a compound of formula (E):

or a pharmaceutically acceptable salt thereof.

In another embodiment, the oligomeric compound of formula (E) is an oligomeric compound of formula (XII):

or a pharmaceutically acceptable salt thereof.

In another embodiment, R³At each occurrence is trityl.

Preparation process of Eteplirsen

Provided herein are methods of making Eteplirsen.

In one aspect, provided herein is a method of making an oligomeric compound of formula (E):

wherein the method comprises the following sequential steps:

(a) contacting a compound of formula (I):

wherein R is¹Is a carrier medium for the carrier medium,

to form a compound of formula (II):

wherein R is¹Is a carrier medium;

(b) contacting a compound of formula (II) with compound (B):

to form a compound of formula (III):

wherein R is¹Is a carrier medium;

(c) contacting a compound of formula (III) with a deblocking agent to form a compound of formula (IV):

wherein R is¹Is a carrier medium;

(d) contacting a compound of formula (IV) with a compound of formula (C):

to form a compound of formula (V):

wherein R is¹Is a carrier medium;

(e) contacting a compound of formula (V) with a deblocking agent to form a compound of formula (VI):

wherein R is¹Is a carrier medium;

(f) contacting a compound of formula (VI) with a compound of formula (F):

to form a compound of formula (VII):

wherein R is¹Is a carrier medium;

(g) 28 iterations of the following sequential steps were performed:

(g1) contacting the product formed in the previous step with a deblocking agent; and is

(g2) Contacting the compound formed in the previous step with a compound of formula (VIII):

wherein R is²For each compound of formula (VIII), independently selected from:

wherein, for 1 to 28 iterations, R²Comprises the following steps:

iteration number	R²	Iteration number	R²	Iteration number	R²
						1	PC	11	DPG	21	PA
2	PC	12	DPG	22	T
						3	PA	13	PA	23	T
4	PA	14	PA	24	T
						5	PC	15	DPG	25	PC
6	PA	16	PA	26	T
						7	T	17	T	27	PA
8	PC	18	DPG	28	DPG
						9	PA	19	DPG
10	PA	20	PC

To form a compound of formula (IX):

wherein R is¹Is a carrier medium for the carrier medium,

wherein R is²For each occurrence, is independently selected from:

and

wherein R is²At each position from 1 to 30 and 5 'to 3':

position Nos. 5 'to 3'	R²	Position Nos. 5 'to 3'	R²	Position Nos. 5 'to 3'	R²
						1	PC	11	PA	21	DPG
2	T	12	PA	22	PC
						3	PC	13	DPG	23	PA
4	PC	14	DPG	24	T
						5	PA	15	PA	25	T
6	PA	16	PA	26	T
						7	PC	17	DPG	27	PC
8	PA	18	PA	28	T
						9	T	19	T	29	PA
10	PC	20	DPG	30	DPG

(h) Contacting a compound of formula (IX) with a deblocking agent to form a compound of formula (X):

wherein R is¹Is a carrier medium for the carrier medium,

wherein R is²For each occurrence, is independently selected from:

and

wherein R is²At each position from 1 to 30 and 5 'to 3':

(i) Contacting a compound of formula (X) with a cleaving agent to form a compound of formula (XI):

wherein R is²For each occurrence, is independently selected from:

and

wherein R is²At each position from 1 to 30 and 5 'to 3':

and

(j) contacting a compound of formula (XI) with a deprotecting agent to form an oligomeric compound of formula (E).

In one embodiment, step (d), step (f), step g (2), or a combination thereof further comprises contacting the compound of formula (IV), the compound of formula (VI), or the compound formed from the previous step, respectively, with an endcapping agent.

In certain embodiments, each of step (d), step (f), step g (2) further comprises contacting the compound of formula (IV), formula (VI), or the compound formed from the previous step, respectively, with an endcapping agent.

In another embodiment, the halogenated acid is trifluoroacetic acid.

In another embodiment, at least one of steps (c), (e1), and (f) further comprises the step of contacting the deblocking compound of each step with a neutralizing agent.

In another embodiment, each of steps (c), (e1), and (f) further comprises the step of contacting the deblocking compound of each step with a neutralizing agent.

In another embodiment, the neutralizing agent is N, N-diisopropylethylamine.

In yet another embodiment, the capping agent is in a solution comprising ethylmorpholine and methylpyrrolidone.

In another embodiment, the capping agent is an anhydride.

In another embodiment, the anhydride is benzoic anhydride.

In another embodiment, the compound of formula (VIII), compound (C) and compound (F) are each independently a solution comprising ethyl morpholine and dimethyl imidazolidinone.

In yet another embodiment, the deprotecting agent comprises NH₃。

In another embodiment, the deprotecting agent is in aqueous solution.

In another embodiment, the compound of formula (C) has formula (C1):

in another embodiment, the compound of formula (V) has formula (Va):

wherein R is¹Is a carrier medium.

In another embodiment, the compound of formula (F) has formula (F1):

in another embodiment, the compound of formula (VII) has formula (VIIa):

wherein R is¹Is a carrier medium.

In another embodiment, the compound of formula (VIII) has formula (VIIIa):

wherein R is²For each compound of formula (VIIIa), independently selected from:

in another embodiment, the compound of formula (IX) has formula (IXa):

or a pharmaceutically acceptable salt thereof, wherein

R¹Is a carrier medium, and

R²independently at each occurrence is selected from

And is

Wherein R is²At each position from 1 to 30 and 5 'to 3':

In another embodiment, the compound of formula (X) has formula (Xa):

or a pharmaceutically acceptable salt thereof, wherein,

R¹is a carrier medium, and

R²independently at each occurrence is selected from:

and is

Wherein R is²At each position from 1 to 30 and 5 'to 3':

In another embodiment, the compound of formula (XI) has formula (XIa):

or a pharmaceutically acceptable salt thereof, wherein:

R²independently at each occurrence is selected from:

and is

Wherein R is²At each position from 1 to 30 and 5 'to 3':

In another embodiment, the compound of formula (VI) has formula (VIa):

wherein R is¹Is a carrier medium.

In yet another embodiment, the oligomeric compound of formula (E) is an oligomeric compound of formula (XII):

in another aspect, provided herein is a compound of formula (a 1):

or a pharmaceutically acceptable salt thereof, wherein:

each R¹Independently a carrier medium; and

each R³Independently selected from hydrogen, trityl, monomethoxytrityl, dimethoxytrityl and trimethoxytrityl.

In another aspect, provided herein is a compound of formula (a 3):

or a pharmaceutically acceptable salt thereof, wherein:

R¹is a carrier medium; and

R³selected from the group consisting of trityl, monomethoxytrityl, dimethoxytrityl and trimethoxytrityl;

in another aspect, provided herein is a compound of formula (a 5):

or a pharmaceutically acceptable salt thereof, wherein R¹Is a carrier medium, R³Selected from the group consisting of trityl, monomethoxytrityl, dimethoxytrityl and trimethoxytrityl, and R⁴Selected from:

in some embodiments, the compound of formula (A5) is formula (A5 a):

or a pharmaceutically acceptable salt thereof, wherein R¹Is a carrier medium, R³Selected from the group consisting of trityl, monomethoxytrityl, dimethoxytrityl and trimethoxytrityl, R⁴Selected from:

in another aspect, provided herein is a compound of formula (V):

or a pharmaceutically acceptable salt thereof, wherein R¹Is a carrier medium.

In some embodiments, the compound of formula (V) is formula (Va):

or a pharmaceutically acceptable salt thereof, wherein R¹Is a carrier medium.

In another aspect, provided herein is a compound of formula (VI):

or a pharmaceutically acceptable salt thereof, wherein R¹Is a carrier medium.

In some embodiments, the compound of formula (VI) is formula (VIa):

or a pharmaceutically acceptable salt thereof, wherein R¹Is a carrier medium.

In another aspect, provided herein is a compound of formula (VII):

or a pharmaceutically acceptable salt thereof, wherein R¹Is a carrier medium.

In some embodiments, the compound of formula (VII) is formula (VIIa):

or a pharmaceutically acceptable salt thereof, wherein R¹Is a carrier medium.

In another aspect, provided herein is a compound of formula (IX):

or a pharmaceutically acceptable salt thereof, wherein R¹Is a carrier medium, and

R²independently at each occurrence is selected from:

and is

R²At each position from 1 to 30 and 5 'to 3':

position Nos. 5 'to 3'	R²	Position Nos. 5 'to 3'	R²	Position Nos. 5 'to 3'	R²
						1	C	11	A	21	G
2	T	12	A	22	C
						3	C	13	G	23	A
4	C	14	G	24	T
						5	A	15	A	25	T
6	A	16	A	26	T
						7	C	17	G	27	C
8	A	18	A	28	T
						9	T	19	T	29	A
10	C	20	G	30	G

In one embodiment, the compound of formula (IX) has formula (IXa):

or a pharmaceutically acceptable salt thereof, wherein

R¹Is a carrier medium, and

R²independently at each occurrence is selected from:

and is

R²At each position from 1 to 30 and 5 'to 3':

In another aspect, provided herein is a compound of formula (a 9):

or a pharmaceutically acceptable salt thereof, wherein:

n is an integer of 10 to 40,

R¹is a carrier medium for the carrier medium,

R⁴each occurrence is independently selected from:

in one embodiment, the compound of formula (A9) has formula (A9 a):

or a pharmaceutically acceptable salt thereof, wherein:

n is an integer of 10 to 40,

R¹is a carrier medium for the carrier medium,

R⁴each occurrence is independently selected from:

in another embodiment, the compound of formula (a9) has formula (IX) as shown above.

In another aspect, provided herein is a compound of formula (X):

or a pharmaceutically acceptable salt thereof, wherein

R¹Is a carrier medium, and

R²independently at each occurrence is selected from:

and is

R²At each position from 1 to 30 and 5 'to 3':

In one embodiment, the compound of formula (X) has formula (Xa):

or a pharmaceutically acceptable salt thereof, wherein

R¹Is a carrier medium, and

R²independently at each occurrence is selected from:

and is

R²At each position from 1 to 30 and 5 'to 3':

In another aspect, there is provided a compound of formula (a 10):

or a pharmaceutically acceptable salt thereof, wherein:

n is an integer of 10 to 40,

R¹is a carrier medium for the carrier medium,

R⁴each occurrence is independently selected from:

in one embodiment, the compound of formula (a10) has the formula (a10 a):

or a pharmaceutically acceptable salt thereof, wherein:

n is an integer of 10 to 40,

R¹is a carrier medium for the carrier medium,

R⁴each occurrence is independently selected from:

in another embodiment, the compound of formula (a10) is a compound of formula (X) as shown above.

In another embodiment of these compounds, the support medium comprises polystyrene with 1% cross-linked divinylbenzene.

In another aspect, there is provided a compound that is formula (XI):

or a pharmaceutically acceptable salt thereof, wherein

R²Independently at each occurrence is selected from:

and is

R²At each position from 1 to 30 and 5 'to 3':

In one embodiment, the compound of formula (XI) has formula (XIa):

or a pharmaceutically acceptable salt thereof, wherein

R²Independently at each occurrence is selected from:

and is

R²At each position from 1 to 30 and 5 'to 3':

In another aspect, provided herein is a compound of formula (a 11):

or a pharmaceutically acceptable salt thereof, wherein:

n is an integer of 10 to 40,

R¹is a carrier medium for the carrier medium,

R⁴each occurrence is independently selected from:

in one embodiment, the compound of formula (a11) has formula (a11 a):

or a pharmaceutically acceptable salt thereof, wherein:

n is an integer of 10 to 40,

R¹is a carrier medium for the carrier medium,

R⁴each occurrence is independently selected from:

in another embodiment, the compound of formula (a11) has the formula (XI) as shown above.

Oligomer

Important properties of morpholino-based subunits include: 1) the ability to link in oligomeric form via a stable, uncharged or positively charged backbone linkage; 2) the ability to support nucleotide bases (e.g., adenine, cytosine, guanine, thymidine, uracil, 5-methyl-cytosine, and hypoxanthine) such that the resulting polymer can hybridize to complementary base target nucleic acids, including target RNAs; 3) the ability of the oligomer to be actively or passively transported into a mammalian cell; 4) the ability of the oligo-and oligomen RNA heteroduplexes to resist RNase and RNase H degradation, respectively.

In some embodiments, the antisense oligomer contains base modifications or substitutions. For example, certain nucleobases can be selected to increase the binding affinity of antisense oligomers described herein. The 5-methylcytosine substitution has been shown to increase nucleic acid duplex stability by 0.6-1.2 ℃ and can be incorporated into antisense oligomers described herein. In one embodiment, at least one of the pyrimidine bases of the oligomer comprises a 5-substituted pyrimidine base, wherein the pyrimidine base is selected from the group consisting of cytosine, thymine, and uracil. In one embodiment, the 5-substituted pyrimidine base is 5-methylcytosine. In another embodiment, at least one purine base of the oligomer comprises hypoxanthine.

Morpholino-based oligomers (including antisense oligomers) are described in detail, for example, in U.S. Pat. nos. 5,698,685, 5,217,866, 5,142,047, 5,034,506, 5,166,315, 5,185,444, 5,521,063, 5,506,337, 8,299,206, and 8,076,476. International patent application publication Nos. WO/2009/064471 and WO/2012/043730, and Summerton et al (1997, Antisense and Nuclear Acid Drug Development,7,187-195), each of which is incorporated herein by reference in its entirety.

Oligomeric Compounds of the disclosure can have asymmetric centers, chiral axes, and chiral faces (e.g., as described in: e.l. eliel and s.h. wilen, Stereo-Chemistry of Carbon Compounds, John Wiley & Sons, new york,1994, p. 1119-. The oligomeric compounds of the invention specifically mentioned herein, without any indication of their stereochemistry, are intended to represent all possible isomers and mixtures thereof.

Specifically, without wishing to be bound by any particular theory, as discussed herein, the oligomeric compounds of the invention are prepared from activated morpholino subunits, including non-limiting examples such as compounds of formula (VIII):

wherein R is²Independently for each compound of formula (VIII), selected from the group consisting of:

each of the compounds of formula (VIII) above may be prepared, for example, from the corresponding β -D-ribofuranosyl group, as shown below:

referring to Summerton et al, Antisense & Nucleic Acid Drug Dev.7:187-195(1997), without being bound by any particular theory, the stereochemistry of the two chiral carbons is preserved under synthetic conditions, allowing the generation of many possible stereoisomers of each morpholino subunit based on the selection of, for example, α -L-ribofuranosyl, α -D-ribofuranosyl, β -L-ribofuranosyl or β -D-ribofuranosyl starting materials.

For example, in some embodiments, the compound of formula (VIII) of the present disclosure may be of formula (VIIIa):

wherein R is²Independently for each compound of formula (VIIIa), selected from the group consisting of:

without being bound by any particular theory, for example, incorporation of 10 to 40 compounds of formula (VIII) into the oligomeric compounds of the present disclosure can yield many possible stereoisomers.

Without wishing to be bound by any particular theory, the oligomeric compounds of the invention comprise one or more phosphorous-containing subunits that generate a chiral center at each phosphorous, each of which is designated as an "Sp" or "Rp" structure as understood in the art. Without wishing to be bound by any particular theory, this chirality produces stereoisomers that have the same chemical composition but differ in the three-dimensional arrangement of their atoms.

Without wishing to be bound by any particular theory, the configuration of each phosphorus intersubunit linkage occurs randomly during synthesis of, for example, the oligomeric compounds of the present disclosure. Without wishing to be bound by any particular theoryIn a further embodiment, the oligomeric compounds of the present disclosure are comprised of a plurality of phosphorus intersubunit linkages, each having a random chiral configuration. In particular, without wishing to be bound by any particular theory, each intersubunit linkage of additional morpholino subunits doubles the number of stereoisomers of the product, such that conventional preparation of oligomeric compounds of the present disclosure is actually 2^NA highly heterogeneous mixture of individual stereoisomers, wherein N represents the number of linkages between phosphorus subunits.

Accordingly, unless otherwise indicated, all such isomers are included, including diastereomers and enantiomeric mixtures, as well as pure enantiomers and diastereomers, for example, when one or more bonds from one or more stereocenters are represented by "-" or "to", or equivalents as understood in the art.

Table 1 describes various embodiments of morpholino subunits provided in the methods described herein.

Table 1: various embodiments of morpholino subunits.

Examples

The following examples are set forth in order to illustrate and describe certain specific embodiments of the present disclosure. However, the scope of the claims is not in any way limited by the examples set forth herein. Various changes and modifications to the disclosed embodiments will be apparent to those skilled in the art, and such changes and modifications may be made without departing from the chemical structures, substituents, derivatives, formulations or methods of the present disclosure, including but not limited to those involving the chemical structures of the present disclosure, substituting for the spirit of the present disclosure and the scope of the appended claims. The definitions of the variables in the structures in the schemes herein are comparable to the definitions of the corresponding positions in the formulae provided herein.

Example 1: NCP2 anchored synthesis

Preparation of methyl 1.4-fluoro-3-nitrobenzoate (1)

To a 100L flask was added 12.7kg of 4-fluoro-3-nitrobenzoic acid, 40kg of methanol and 2.82kg of concentrated sulfuric acid. The mixture was stirred at reflux (65 ℃) for 36 hours. The reaction mixture was cooled to 0 ℃. Crystals formed at 38 ℃. The mixture was kept at 0 ℃ for 4 hours and then filtered under nitrogen. The 100L flask was washed with 10kg of methanol which had been cooled to 0 ℃ and the filter cake was washed. The solid filter cake was dried on the funnel for 1 hour, transferred to a tray, and dried in a vacuum oven at room temperature to a constant weight of 13.695kg of methyl 4-fluoro-3-nitrobenzoate (100% yield; HPLC 99%).

Preparation of 3-nitro-4- (2-oxopropyl) benzoic acid

(Z) -4- (3-hydroxy-1-methoxy-1-oxobut-2-en-2-yl) -3-nitrobenzoic acid methyl ester (2)

To a 100L flask were charged 3.98kg of methyl 4-fluoro-3-nitrobenzoate (1) from the previous step, 9.8kg of DMF, 2.81kg of methyl acetoacetate. The mixture was stirred and cooled to 0 ℃. 3.66kg of DBU was added thereto over about 4 hours while maintaining the temperature at 5 ℃ or below 5 ℃. The mixture was stirred for an additional 1 hour. A solution of 8.15kg of citric acid in 37.5kg of purified water was added to the reaction flask while maintaining the reaction temperature at 15 ℃ or below 15 ℃. After addition, the reaction mixture was stirred for an additional 30 minutes and then filtered under nitrogen. The wet cake was placed back in a 100L flask along with 14.8kg of purified water. The slurry was stirred for 10 minutes and then filtered. The wet cake was placed back in the 100L flask again, slurried with 14.8kg of purified water for 10 minutes, and filtered to give crude methyl (Z) -4- (3-hydroxy-1-methoxy-1-oxobut-2-en-e-methyl ester) pyridin-2-yl) -3-nitrobenzoate.

B.3-Nitro-4- (2-oxopropyl) benzoic acid

The crude (Z) -4- (3-hydroxy-1-methoxy-1-oxobut-2-en-2-yl) -3-nitrobenzoate was charged to a 100L reaction flask under nitrogen. 14.2kg of 1, 4-dioxane were added thereto and stirred. A solution of 16.655kg of concentrated HCl and 13.33kg of purified water (6M HCl) was added to the mixture over 2 hours while maintaining the temperature of the reaction mixture below 15 ℃. After the addition was complete, the reaction mixture was heated to reflux (80 ℃) for 24 hours, cooled to room temperature, and filtered under nitrogen. The solid filter cake was triturated with 14.8kg purified water, filtered, triturated again with 14.8kg purified water, and filtered. The solid was returned to a 100L flask with 39.9kg DCM and refluxed for 1 hour with stirring. 1.5 kg of purified water was added to dissolve the remaining solids. The bottom organic layer was separated into a preheated 72L flask and then returned to a clean dry 100L flask. The solution was cooled to 0 ℃ for 1 hour and then filtered. The solid filter cake was washed twice with solutions of 9.8kg each of DCM and 5kg of heptane and then dried on the funnel. The solid was transferred to a tray and dried to a constant weight of 1.855kg to give 3-nitro-4- (2-oxopropyl) benzoic acid. The total yield of compound 1 was 42%. HPLC 99.45%.

Preparation of N-tritylpiperazine succinate (NTP)

To a 72L jacketed flask, under nitrogen, were added 1.805kg of trityl chloride and 8.3kg of toluene (TPC solution). The mixture was stirred until the solid dissolved. To a 100L jacketed reaction flask, 5.61kg of piperazine, 19.9kg of toluene and 3.72kg of methanol were added under nitrogen. The mixture was stirred and cooled to 0 ℃. The TPC solution was slowly added in portions over 4 hours while maintaining the reaction temperature at 10 ℃ or below 10 ℃. The mixture was stirred at 10 ℃ for 1.5 hours and then warmed to 14 ℃. 32.6kg of purified water was added to a 72L flask and then transferred to a 100L flask while maintaining the internal batch temperature at 20+/-5 ℃. The layers were separated, the bottom aqueous layer was separated and stored. The organic layer was extracted three times with 32kg of pure water, respectively, and the aqueous layer was separated and combined with the stored aqueous solution.

The remaining organic layer was cooled to 18 ℃ and a solution of 847g of succinic acid in 10.87kg of purified water was slowly added in portions to the organic layer. The mixture was stirred at 20+/-5 ℃ for 1.75 hours. The mixture was filtered and the solid was washed with 2kg TBME and 2kg acetone and then dried on the funnel. The filter cake was triturated twice with 5.7kg each of acetone, filtered and washed with 1kg of acetone between triturations. The solid was dried on a funnel and then transferred to a tray and dried in a vacuum oven at room temperature to a constant weight of 2.32kg NTP. The yield thereof was found to be 80%.

Preparation of (4- (2-hydroxypropyl) -3-nitrophenyl) (4-tritylpiperazin-1-yl) methanone

A. Preparation of 1- (2-nitro-4- (4-tritylpiperazine-1-carbonyl) phenyl) propan-2-one

To a 100L jacketed flask was added 2kg of 3-nitro-4- (2-oxopropyl) benzoic acid (3), 18.3kg of DCM, 1.845kg of N- (3-dimethylaminopropyl) -N' -ethylcarbodiimide hydrochloride (EDC. HCl) under nitrogen. The solution was stirred until a homogeneous mixture was formed. 3.048kg NTP was added over 30 minutes at room temperature and stirred for 8 hours. 5.44kg of purified water was added to the reaction mixture and stirred for 30 minutes. The layers were separated and the bottom organic layer containing the product was drained and stored. The aqueous layer was extracted twice with 5.65kg DCM. The combined organic layers were washed with a solution of 1.08kg sodium chloride in 4.08kg purified water. The organic layer was dried over 1.068kg sodium sulfate and filtered. The sodium sulfate was washed with 1.3kg of DCM. The combined organic layers were slurried with 252g of silica gel and filtered through a filter funnel containing 252g of silica gel bed. The silica bed was washed with 2kg of DCM. The combined organic layers were evaporated on a rotary evaporator. 4.8kg of THF are added to the residue, which is then evaporated on a rotary evaporator until 2.5 volumes of crude 1- (2-nitro-4- (4-tritylpiperazine-1-carbonyl) phenyl) propan-2-one in THF are reached.

B. Preparation of (4- (2-hydroxypropyl) -3-nitrophenyl) (4-tritylpiperazin-1-yl) methanone (5)

3600g of compound 4 from the previous step and 9800g of THF were charged to a 100L jacketed flask. Cooling the stirred solution to be less than or equal to 5 ℃. The solution was diluted with 11525g of ethanol and 194g of sodium borohydride were added at ≤ 5 deg.C over a period of about 2 hours. The reaction mixture was stirred at <5 ℃ for a further 2 hours. The reaction was quenched by slowly adding a solution of about 1.1kg ammonium chloride in about 3kg water to maintain the temperature at ≦ 10 ℃. The reaction mixture was stirred for an additional 30 minutes, filtered to remove inorganic material, and charged into a 100L jacketed flask and extracted with 23kg DCM. The organic layer was separated and the aqueous layer was extracted twice with 4.7kg each of DCM. The combined organic layers were washed with a solution of about 800g of sodium chloride in about 3kg of water and then dried over 2.7kg of sodium sulfate. The suspension was filtered and the filter cake was washed with 2kg of DCM. The combined filtrates were concentrated to 2.0 volumes, diluted with about 360g of ethyl acetate and evaporated. The crude product was loaded onto a silica column of 4kg silica, which was packed with DCM under nitrogen and eluted with 2.3kg ethyl acetate in 7.2kg DCM. The combined fractions were evaporated and the residue was dissolved in 11.7kg of toluene. The toluene solution was filtered and the filter cake was washed twice with 2kg of toluene. The filter cake was dried to a constant weight of 2.275kg to give compound 5 (46% yield from compound 3) HPLC 96.99%.

Preparation of 2, 5-dioxopyrrolidin-1-yl (1- (2-nitro-4- (4-triphenylmethylpiperazine-1-carbonyl) phenyl) propan-2-yl) carbonate (NCP2 anchor)

To a 100L jacketed flask, 4.3kg of Compound 5 (via H) was added under nitrogen¹NMR adjusted weight based on residual toluene; all reagents scaled accordingly thereafter) and 12.7kg pyridine. Thereto was added 3.160kg DSC (78.91 wt%, by H)¹NMR) while maintaining the internal temperature at 35 ℃ or less. The reaction mixture was aged at ambient for about 22 hours and then filtered. The filter cake was washed with 200g pyridine. In two batches containing 1/2 volumes of filtrate, the filtrate was slowly added to a 100L jacketed flask containing a solution of about 11kg of citric acid in about 50kg of water and stirred for 30 minutes to effect precipitation of a solid. The solid was collected on a filter funnel, washed twice with 4.3kg of water per wash and dried under vacuum on the filter funnel.

The combined solids were charged to a 100L jacketed flask and dissolved in 28kg DCM and washed with a solution of 900g potassium carbonate in 4.3kg water. After 1 hour, the layers were separated and the aqueous layer was removed. The organic layer was washed with 10kg of water, separated and dried over 3.5kg of sodium sulfate. DCM was filtered, evaporated and dried under vacuum to 6.16kg yielding NCP2 anchor (114% yield).

Example 2: synthesis of anchoring resins

To a 75L solid phase synthesis reactor with a Teflon stop cock was added about 52L NMP and 2300g of aminoethylpolystyrene resin. The resin was stirred in NMP to swell for about 2 hours and then drained. The resin was washed twice with about 4LDCM per wash, then twice with 39L of neutralizing solution per wash, and then twice with 39LDCM per wash. The NCP2 anchoring solution was slowly added to the stirred resin solution, stirred at room temperature for 24 hours, and drained. The resin was washed four times with 39L of NMP for each wash and six times with 39LDCM for each wash. The resin was treated and stirred with 1/2DEDC capping solution for 30 minutes, drained, and treated with a second 1/2DEDC capping solution for 30 minutes and stirred and drained. The resin was washed six times with 39LDCM each time and then dried in an oven to a constant weight of 3573.71g to give an anchoring resin.

Example 3: preparation of activated EG3 Tail (see FIG. 2)

1. Preparation of Triphenylmethylpiperazine phenyl carbamate 35

To the cooled suspension of NTP in dichloromethane (6mL/g NTP) was added a solution of potassium carbonate (3.2 equivalents) in water (4mL/g potassium carbonate). To the biphasic mixture was slowly added a solution of phenyl chloroformate (1.03 equiv) in dichloromethane (2g/g phenyl chloroformate). The reaction mixture was warmed to 20 ℃. After completion of the reaction (1-2 hours), the layers were separated. The organic layer was washed with water and dried over anhydrous potassium carbonate. Product 35 was isolated by crystallization from acetonitrile. The yield was 80%.

2. Preparation of Carbamate 36

Sodium hydride (1.2 equivalents) was suspended in 1-methyl-2-pyrrolidone (32mL/g sodium hydride). To this suspension was added triethylene glycol (10.0 equivalents) and compound 35(1.0 equivalent). The resulting slurry was heated to 95 ℃. After completion of the reaction (1-2 hours), the mixture was cooled to 20 ℃. To this mixture was added 30% methylene chloride/methyl t-butyl ether (v: v) and water. The organic layer containing the product was washed successively with aqueous NaOH solution, aqueous succinic acid solution and saturated aqueous sodium chloride solution. Product 36 was isolated by crystallization from dichloromethane/methyl tert-butyl ether/heptane. The yield was 90%.

3. Preparation of EG3 Tail acid 37

To a solution of compound 36 in tetrahydrofuran (7mL/g 36) was added succinic anhydride (2.0 equiv.) and DMAP (0.5 equiv.). The mixture was heated to 50 ℃. After completion of the reaction (5 hours), the mixture was cooled to 20 ℃ and NaHCO was used₃The aqueous solution was adjusted to pH 8.5. Methyl tert-butyl ether was added and the product was extracted into the aqueous layer. Dichloromethane was added and the mixture was adjusted to pH3 with aqueous citric acid. The organic layer containing the product was washed with a mixture of citrate buffer at pH3 and saturated aqueous sodium chloride solution. In the preparation of compound 38, a dichloromethane solution of 37 was used without isolation.

4. Preparation of activated EG3 Tail 38

To the solution of compound 37 was added N-hydroxy-5-norbornene-2, 3-dicarboxylic acid imide (HONB) (1.02 equiv.), 4-Dimethylaminopyridine (DMAP) (0.34 equiv.), followed by 1- (3-dimethylaminopropyl)) -N' -ethylcarbodiimide hydrochloride (EDC) (1.1 equiv.). The mixture was heated to 55 ℃. After completion of the reaction (4-5 hours), the mixture was cooled to 20 ℃ and washed with 1:1 of 0.2M citric acid/brine and brine in that order. The dichloromethane solution was solvent exchanged with acetone and then with N, N-dimethylformamide and the product was isolated by precipitation from acetone/N, N-dimethylformamide into a saturated aqueous sodium chloride solution. The crude product was reslurried several times in water to remove residual N, N-dimethylformamide and salts. The yield from compound 36 to tail 38 of activated EG3 was 70%.

Example 4: 50L solid phase Synthesis of Eteplirsen [ oligomeric Compound (XII) ] feedstock drug

1. Raw materials

Table 2: starting materials

Chemical structure of raw material:

A. activated tail of EG3

B. Activated subunit C (for preparation, see U.S. Pat. No. 8,067,571)

C. Activated subunit A (for preparation, see U.S. Pat. No. 8,067,571)

D. Activated DPG subunits (for preparation, see WO2009/064471)

E. Activated T subunit (for preparation, see WO2013/082551)

F. Anchoring resin

Wherein R is¹Is a carrier medium.

Table 3: description of solutions for solid phase oligomer Synthesis of Eteplissen raw drug

Name of solution	Composition of solution
		NCP2 Anchor solution	37.5L NMP and 1292g NCP2 Anchor
DEDC capping solution	4.16L Pyrocarbonic acid Diethyl Ester (DEDC), 3.64L NEM, and 33.8L DCM
		CYTFA solution	2.02kg 4-cyanopyridine, 158L DCM, 1.42L TFA, 39L TFE, and 2L pure water
Neutralizing solution	35.3L IPA, 7.5L DIPEA, and 106.5L DCM
		CrackingSolutions of	1,530.04g DTT, 6.96L NMP, and 2.98L DBU

Synthesis of Eteplirsen drug substance

A. Resin expansion

750g of the loaded anchor resin and 10.5L of LNMP were charged to a 50L silylation reactor and stirred for 3 hours. NMP was drained and the anchoring resin was washed twice with 5.5L each time of DCM and twice with 5.5L each time of 30% TFE/DCM.

B. And (3) circulation 0: EG3 tail coupling

The anchoring resin was washed three times with 5.5L 30% TFE/DCM each time and drained, washed with 5.5L CYFTA solution for 15 minutes and drained, washed again with 5.5L CYTFA solution for 15 minutes without draining, 122mL of 1:1NEM/DCM were added thereto and the suspension was stirred for 2 minutes and drained. The resin was washed twice with 5.5L of the neutralized solution for 5 minutes and drained, then twice with 5.5L each of DCM and drained. A3 LDMI solution containing 706.2g of activated EG3 tail (MW 765.85) and 234mLNEM was added to the resin and stirred at room temperature for 3 hours and drained. The resin was washed twice with 5.5L each time of a neutralization solution for 5 minutes each time and once with 5.5L DCM and drained. A solution of 374.8g of benzoic anhydride and 195mL of NEM in 2680mL of NMP was stirred for 15 minutes and drained. The resin was stirred with 5.5L of the neutralized solution for 5 minutes, then washed once with 5.5L of LDCM and twice with 5.5L portions of 30% TFE/DCM. The resin was suspended in 5.5L of 30% TFE/DCM and held for 14 hours.

C. Subunit coupling cycle 1-30

i. Pre-coupling treatment

Before each coupling cycle, as described in table 4, the resin: 1) washed with 30% TFE/DCM; 2) a) treating with CYTFA solution for 15 minutes and draining, and b) treating with CYTFA solution for 15 minutes, adding 1:1NEM/DCM thereto, stirring and draining; 3) stirring with the neutralizing solution for three times; 4) washed twice with DCM. See table 4.

Post-coupling treatment

After draining each subunit solution, as described in table 4, the resin: 1) washing with DCM; 2) washed twice with 30% TFE/DCM. If the resin is held for a period of time before the next coupled cycle, the second TFE/DCM wash is not drained and the resin remains in the TFE/DCM wash solution. See table 4.

Activation subunit coupled cycle

The coupling cycle was performed as described in table 4.

Final IPA wash

After the final coupling step as described in Table 4, the resin was washed 8 times with 19.5L each of IPA and dried under vacuum at room temperature for about 63.5 hours at 5,579.8g dry weight.

C. Cracking

The resin-bound Eteplisen stock drug described above was divided into two batches, each batch processed as follows: 2,789.9g of resin: 1) stirred with 10L of NMP for 2 hours, then NMP was discharged; 2) washed three times with 10L each time of 30% TFE/DCM; 3) treatment with 10L CYTFA solution for 15 min; 4)10L CYTFA solution for 15 min, then 130ml 1:1NEM/DCM were added, stirred for 2 min and drained. The resin was treated three times with 10L of neutralizing solution each time, washed six times with 10L of DCM and eight times with 10L of NMP each time. The resin was treated with 1530.4g DTT and 2980DBU in 6.96L NMP for 2 hours to isolate the Eteplisen prodrug from the resin. The lysis solution was drained and retained in a separate container. The reactor and resin were washed with 4.97l nmp and combined with the lysis solution.

Table 4:

table 4 (continuation)

Table 4 (continuation)

D. Deprotection of the amino acid

The combined lysis solution and NMP wash were transferred to a pressure vessel, to which 39.8L NH was added₄OH(NH₃·H₂O), which has been cooled in a freezer to a temperature of-10 ℃ to-25 ℃. Pressure vesselThe vessel was sealed and heated to 45 ℃ for 16 hours, then cooled to 25 ℃. The deprotected solution containing the Eteplirsen starting drug was diluted 3:1 with purified water and the pH adjusted to 3.0 with 2M phosphoric acid, then NH₄OH was adjusted to pH 8.03. HPLC (C18) 73-74% (FIG. 1).

TABLE 5 data from FIG. 1

Example 5: purification of Eteplirsen raw drug

The deprotected solution containing the Eteplissen starting drug substance from section D of example 2 was loaded onto a ToyoPearl Super-Q650S anion exchange resin column (Tosohbioscience) and the fractions of acceptable purity (C18 and SCXHPLC) were combined into the purified drug product solution, eluting with a 17 column volume gradient of 0-35% B (buffer A: 10mM sodium hydroxide; buffer B: 1M sodium chloride in 10mM sodium hydroxide). HPLC (fig. 2): 97.74% (C18) 94.58% (SCX).

The purified drug solution was desalted and lyophilized to 1959g of purified Eteplirsen drug. The yield is 61.4%; HPLC (fig. 3): 97.7% (C18) 94.6% (SCX).

TABLE 6 data of FIG. 2

TABLE 7 data of FIG. 3

TABLE 8 abbreviations

Abbreviations	Name (R)
		DBU	1, 8-diazabicycloundec-7-enes
DCM	Methylene dichloride
		DIPEA	N, N-diisopropylethylamine
DMI	1, 3-dimethyl-2-imidazolidinone
		DTT	Dithiothreitol
IPA	Isopropanol (I-propanol)
		MW	Molecular weight
NEM	N-ethyl morpholine
		NMP	N-methyl-2-pyrrolidone
RT	At room temperature
		TFA	2,2, 2-trifluoroacetic acid
TFE	2,2, 2-trifluoroethanol

Is incorporated by reference

The contents of all references (including journal articles, issued patents, published patent applications, and co-pending patent applications) cited in this application are hereby expressly incorporated herein in their entirety. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art.

Equivalents of

Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the disclosure described herein. Such equivalents are intended to be encompassed by the following claims.

Claims

1. A process for preparing an oligomeric compound of formula (a):

wherein n is an integer of 10 to 40, and each R²Independently at each occurrence, selected from the group consisting of:

wherein the method comprises the following sequential steps:

(a) contacting (a1) with deblocking agent:

wherein R is¹Is a carrier medium, and R³Selected from the group consisting of trityl, monomethoxytrityl, dimethoxytrityl and trimethoxytrityl,

to form a compound of formula (II):

wherein R is¹Is a carrier medium;

(b) contacting a compound of formula (II) with a compound of formula (a 2):

to form a compound of formula (a 3):

wherein R is¹Is a carrier medium, R³Selected from the group consisting of trityl, monomethoxytrityl, dimethoxytrityl, and trimethoxytrityl;

(c) contacting the compound of formula (a3) with a deblocking agent to form a compound of formula (IV):

whereinR¹Is a carrier medium;

(d) contacting a compound of formula (IV) with a compound of formula (a 4):

wherein R is³Is selected from the group consisting of trityl, monomethoxytrityl, dimethoxytrityl and trimethoxytrityl, and R⁴Selected from the group consisting of:

to form a compound of formula (a 5):

R⁴selected from:

(e) n-1 iterations of the following sequential steps are performed:

(e2) Contacting the compound formed in the previous step with a compound of formula (A8):

wherein R is³Selected from the group consisting of trityl, monomethoxytrityl, dimethoxytrityl and trimethoxytrityl, and for each compound of formula (A8), R⁴Independently selected fromThe group consisting of:

to form a compound of formula (a 9):

wherein n is an integer of 10 to 40, R¹Is a carrier medium, R³Is selected from the group consisting of trityl, monomethoxytrityl, dimethoxytrityl and trimethoxypentyl, and R⁴Each occurrence is independently selected from the group consisting of:

and

wherein n is an integer of 10 to 40, R¹Is a carrier medium, and R⁴Each occurrence is independently selected from the group consisting of:

wherein n is an integer of 10 to 40, and R⁴Each occurrence is independently selected from the group consisting of:

and

(j) contacting a compound of formula (a11) with a deprotection agent to form an oligomeric compound of formula (a).

2. The method of claim 1, wherein the compound of formula (A4) has formula (A4 a):

wherein R is³Is selected from the group consisting of trityl, monomethoxytrityl, dimethoxytrityl and trimethoxytrityl, and R⁴Selected from:

3. the method of claim 1 or 2, wherein the compound of formula (A5) is of formula (A5 a):

wherein:

R¹is a carrier medium for the carrier medium,

R³selected from trityl, monomethoxytrityl, dimethoxytritylBenzyl and trimethoxytrityl, and

R⁴selected from:

4. the method of any one of claims 1-3, wherein the compound of formula (A8) is of formula (A8 a):

wherein:

R⁴independently at each occurrence of the compound of formula (A8a) is selected from the group consisting of:

5. the method of any one of claims 1-4, wherein the compound of formula (A9) has formula (la)

Wherein:

n is an integer of 10 to 40,

R¹is a carrier medium for the carrier medium,

R⁴each occurrence is independently selected from the group consisting of:

6. the method of any one of claims 1-5, wherein the compound of formula (A10) is of formula (A10 a):

wherein,

n is an integer of 10 to 40,

R¹is a carrier medium, and

R⁴each occurrence is independently selected from the group consisting of:

7. the method of any one of claims 1-6, wherein the compound of formula (A11) is of formula (A11 a):

wherein:

n is an integer of 10 to 40, and

R⁴each occurrence is independently selected from the group consisting of:

8. the method according to any one of claims 1-7, wherein for the oligomeric compound of formula (A), n is 30, and R is²At each position from 1 to 30 and 5 'to 3':

wherein the oligomeric compound of formula (A) is a compound of formula (E):

or a pharmaceutically acceptable salt thereof.

9. The method of claim 8, wherein the oligomeric compound of formula (E) is an oligomeric compound of formula (XII):

or a pharmaceutically acceptable salt thereof.

10. The process according to claim 1 for preparing oligomeric compounds of formula (E):

wherein the method comprises the following sequential steps:

(a) contacting a compound of formula (I) with a deblocking agent:

wherein R is¹Is a carrier medium for the carrier medium,

to form a compound of formula (II):

wherein R is¹Is a carrier medium;

(b) contacting a compound of formula (II) with compound (B):

to form a compound of formula (III):

wherein R is¹Is a carrier medium;

(d) contacting a compound of formula (IV) with a compound of formula (C):

to form a compound of formula (V):

wherein R is¹Is a carrier medium;

(f) contacting a compound of formula (VI) with a compound of formula (F):

to form a compound of formula (VII):

wherein R is¹Is a carrier medium;

(g) 28 iterations of the following sequential steps were performed:

wherein R is²For each compound of formula (VIII), independently selected from the group consisting of:

wherein, for each iteration from 1 to 28, R²Comprises the following steps:

to form a compound of formula (IX):

wherein R is¹Is a carrier medium for the carrier medium,

wherein R is²For each occurrence, is independently selected from the group consisting of:

and

wherein R is²At each position from 1 to 30 and 5 'to 3':

wherein R is¹Is a carrier medium for the carrier medium,

and

wherein R is²At each position from 1 to 30 and 5 'to 3':

and

wherein R is²At each position from 1 to 30 and 5 'to 3':

and

(j) contacting a compound of formula (XI) with a deprotection agent to form an oligomeric compound of formula (E).

11. The method of any one of claims 1-10, wherein step (d) or step (e2) further comprises contacting the compound of formula (IV) or the compound formed in the previous step, respectively, with an endcapping agent.

12. The process according to any one of claims 1 to 11, wherein the deblocking agent used in each step is a halogenated acid or cyanoacetic acid.

13. The method of claim 12, wherein the halogenated acid is selected from the group consisting of chloroacetic acid, dichloroacetic acid, trichloroacetic acid, fluoroacetic acid, difluoroacetic acid, and trifluoroacetic acid.

14. The method of any one of claims 1-13, wherein at least one of steps (a), (c), (e1), and (f) further comprises the step of contacting the deblocking compound of each step with a neutralizing agent.

15. The method of any one of claims 1-14, wherein the support medium comprises a material selected from the group consisting of glass, modified or functionalized glass, plastic (including acrylics, polystyrene (e.g., polystyrene with 1% cross-linked divinylbenzene), copolymers of styrene and other materials, polypropylene, polyethylene, polybutylene, polyurethane, and teflon), polysaccharides, nylon or nitrocellulose, ceramics, resins, silica or silica-based materials (including silicon and modified silicon), carbon, metals, and fiber optic strands.

16. One selected from the group consisting of formula (a 1):

and formula (A3)

A compound of group consisting of or a pharmaceutically acceptable salt thereof, wherein:

each R¹Independently a carrier medium; and is

Each R³Independently selected from the group consisting of hydrogen, trityl, monomethoxytrityl, dimethoxytrityl and trimethoxytrityl.

17. A compound of formula (A5):

or a pharmaceutically acceptable salt thereof, wherein:

R¹is a carrier medium;

R³selected from the group consisting of hydrogen, trityl, monomethoxytrityl, dimethoxytrityl and trimethoxytrityl; and

R⁴independently at each occurrence, selected from the group consisting of:

18. the compound of claim 17, wherein the compound of formula (A5) is of formula (A5 a):

wherein:

R¹is a carrier medium;

R³selected from the group consisting of trityl, monomethoxytrityl, dimethoxytrityl, and trimethoxytrityl; and

R⁴selected from:

19. the compound of claim 18, wherein R³Is trityl.

20. A compound of formula (A9):

or a pharmaceutically acceptable salt thereof, wherein:

n is an integer of 10 to 40;

R¹is a carrier medium;

R³selected from the group consisting of hydrogen, trityl, monomethoxytrityl, dimethoxytrityl and trimethoxytrityl; and is

R⁴Independently at each occurrence, selected from the group consisting of:

21. the compound of claim 20, wherein the compound of formula (A9) is of formula (A9 a):

wherein:

n is an integer of 10 to 40,

R¹is a carrier medium

R³Is selected from the group consisting of trityl, monomethoxytrityl, dimethoxytrityl and trimethoxytrityl, and

R⁴each occurrence is independently selected from the group consisting of:

22. the compound of claim 20, wherein the compound of formula (a9) is of formula (IX):

or a pharmaceutically acceptable salt thereof, wherein:

R¹is a carrier medium, and

R²independently at each occurrence, selected from the group consisting of:

and is

Wherein R is²At each position from 1 to 30 and 5 'to 3':

23. the compound of claim 22, wherein the compound of formula (IX) is of formula (IXa):

or a pharmaceutically acceptable salt thereof, wherein

R¹Is a carrier medium, and

R²independently at each occurrence, selected from the group consisting of:

and is

Wherein R is²At each position from 1 to 30 and 5 'to 3':

24. the compound of claim 20, wherein the compound of formula (a9) is of formula (Xa):

or a pharmaceutically acceptable salt thereof, wherein

R¹Is a carrier medium, and

R²independently at each occurrence, selected from the group consisting of:

and is

Wherein R is²At each position from 1 to 30 and 5 'to 3':

25. the compound of any one of claims 16-24, wherein the support medium comprises polystyrene.

26. A compound of formula (A11):

or a pharmaceutically acceptable salt thereof, wherein:

n is an integer of 10 to 40;

R¹is a carrier medium;

R³selected from the group consisting of trityl, monomethoxytrityl, dimethoxytrityl, and trimethoxytrityl; and is

R⁴Independently at each occurrence, selected from the group consisting of:

27. the compound of claim 26, wherein the compound of formula (a11) is of formula (a11 a):

or a pharmaceutically acceptable salt thereof, wherein:

n is an integer of 10 to 40;

R¹is a carrier medium;

R⁴Independently at each occurrence, selected from the group consisting of:

28. the compound of claim 26, wherein the compound of formula (a11) is of formula (XI):

or a pharmaceutically acceptable salt thereof, wherein:

R²independently at each occurrence, selected from the group consisting of:

and is

Wherein R is²At each position from 1 to 30 and 5 'to 3':

29. the compound of claim 28, wherein the compound of formula (XI) is of formula (XIa):

or a pharmaceutically acceptable salt thereof, wherein

R²Independently at each occurrence, selected from the group consisting of:

and is

Wherein R is²At each position from 1 to 30 and 5 'to 3':